//Written by Paul Stothard, University of Alberta, Canada

function dnaStats (theDocument) {	

	var newDna = "";
	var title = "";
	var maxInput = 500000;

	if (testScript() == false) {
		return false;
	}

	if ((checkFormElement (theDocument.forms[0].elements[0]) == false) || (checkSequenceLength(theDocument.forms[0].elements[0].value, maxInput) == false))	{
		return false;
	}
	
	var itemsToCheck = ["/g/ (g)1", "/a/ (a)1", "/t/ (t)1", "/c/ (c)1", "/n/ (n)1", "/u/ (u)1", "/r/ (r)1", "/y/ (y)1", "/s/ (s)1", "/w/ (w)1", "/k/ (k)1", "/m/ (m)1", "/b/ (b)1", "/d/ (d)1", "/h/ (h)1", "/v/ (v)1", "/g(?=g)/ (gg)2", "/g(?=a)/ (ga)2", "/g(?=t)/ (gt)2", "/g(?=c)/ (gc)2", "/g(?=n)/ (gn)2", "/a(?=g)/ (ag)2", "/a(?=a)/ (aa)2", "/a(?=t)/ (at)2", "/a(?=c)/ (ac)2", "/a(?=n)/ (an)2", "/t(?=g)/ (tg)2", "/t(?=a)/ (ta)2", "/t(?=t)/ (tt)2", "/t(?=c)/ (tc)2", "/t(?=n)/ (tn)2", "/c(?=g)/ (cg)2", "/c(?=a)/ (ca)2", "/c(?=t)/ (ct)2", "/c(?=c)/ (cc)2", "/c(?=n)/ (cn)2", "/n(?=g)/ (ng)2", "/n(?=a)/ (na)2", "/n(?=t)/ (nt)2", "/n(?=c)/ (nc)2", "/n(?=n)/ (nn)2", "/g|c/ (g,c)1", "/a|t/ (a,t)1", "/r|y|s|w|k/ (r,y,s,w,k)1", "/b|h|d|v|n/ (b,h,d,v,n)1", "/r|y|s|w|k|m|b|d|h|v|n/ (r,y,s,w,k,m,b,d,h,v,n)1"];
	
	openWindow("DNA Stats");
	
	var arrayOfFasta = getArrayOfFasta (theDocument.forms[0].elements[0].value);

	for (var i = 0; i < arrayOfFasta.length; i++)	{
		newDna = getSequenceFromFasta (arrayOfFasta[i]);
		title = getTitleFromFasta (arrayOfFasta[i]);

		newDna = removeNonDna(newDna);

		outputWindow.document.write(getInfoFromTitleAndSequence(title, newDna));

		writeSequenceStats (newDna, itemsToCheck);

		outputWindow.document.write ('<br />\n<br />\n');
	}

	closeWindow();
	return true;
}